Photocleavage method and apparatus to clean fluidic devices

ABSTRACT

A method and system for improving throughput of a fluidic system such as a biopolymer analysis system by cleaning accumulated or clogging biopolymer from the fluidic system is disclosed. The method and system utilize a light energy source to photocleave the biopolymer molecules that may accumulate or aggregate in the fluidic system or clog a passageway. The accumulated biopolymer may be exposed to a light energy source for a sufficient period of time such that the biopolymer molecule is dosed with sufficient energy to photocleave the biopolymer molecules, thereby restoring the efficiency of and flow through the system.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No.15/507,416 filed Feb. 28, 2017, which is the U.S. National Phase under35 U.S.C. § 371 of International Application No. PCT/US2015/047688 filedAug. 31, 2015 designating the U.S.; which claims the benefit of U.S.Provisional Application No. 62/044,823, filed Sep. 2, 2014. Theentireties of these listed applications are incorporated by referenceherein.

BACKGROUND Field

The present disclosure relates to the field of nanotechnology and, morespecifically, to linearizing molecules in nanofluidic and microfluidicchannels.

Description of the Related Art

Biopolymers, such as proteins, DNA, or RNA, are often in the form ofsemi-flexible entwined polymeric chains. These macromolecules arenormally assumed to have a random coil configuration in free solution.For double stranded DNA (dsDNA) in biological solution, the persistencelength (a parameter defining its rigidity) is typically about 50 nm. Inorder to achieve consistent and accurate characterization of DNA andother biopolymers, it is often desirable that the biopolymer be movedthrough a fluidic channel to facilitate analysis or use of thebiopolymer. In some instances, the biopolymer is linearized in achannel; in others, the biopolymer is directed through a fluidic flowpath for other purposes. Further, to facilitate characterization ofmacromolecules and biopolymers, such as DNA, sequences or features ofthe macromolecule may be marked, for example, with fluorescent labelingtechniques. Linearized, labeled biopolymers can then be optically imagedto provide certain information. However, optical mapping techniques forbiopolymers have been hindered by low information density for opticalmaps, and conventional techniques provide only low-throughputcapabilities. Although systems and methods for linearization and opticalmapping providing an accurate, high-throughput characterization ofbiopolymer molecules are becoming more common, these systems are oftenhindered by the reduced throughput over time due to clogging of fluidicpassageways, for example entrances into nanochannel or microchannelregions of nanofluidic and/or microfluidic linearizing systems includingmicrofabricated structures such as pillar arrays. This clogging mayoccur regardless of whether the system is heavily loaded with DNA chainsor lightly loaded, though in lightly loaded systems, the clogging mayoccur at a slower rate. Thus, systems and methods for cleaning andunclogging fluidic systems that handle biopolymers are needed.

SUMMARY

The systems, methods, and devices of the invention each have severalaspects, no single one of which is solely responsible for its desirableattributes. Without limiting the scope of this invention as expressed bythe claims which follow, some features will now be discussed briefly.After considering this discussion, and particularly after reading thesection entitled “Detailed Description,” one will understand how thefeatures of the various embodiments of this invention provide advantagesthat include improved cleaning and increased throughput.

One aspect of this disclosure provides a method for enhancing fluidflow. In one aspect, the method includes moving biopolymer moleculesinto contact with at least one fluidic channel in or on a device,whereby clogging occurs in the device due to coiling or aggregation ofthe biopolymer molecules or adsorption to or tangling around thechannels or any other nano- or micro-patterned features inside thechannel or fluidic device, and directing a light source at a region ofthe device in which said clogging has occurred in a manner effective tophotocleave biopolymers that contribute to said clogging, therebyfacilitating removal or reduction of said clogging. In some aspects, themethod further includes applying a motive force to fluid in the regionof the device in a manner effective to flush the photocleaved biopolymermolecules from the region of the device comprising said clogging. Insome aspects, the motive force may comprise an electrostatic force, apneumatic force, a capillary force, or any combination thereof. In someaspects, the directing a light source comprises directing a light sourcehaving a wavelength of one of about 473 nm or about 488 nm to exciteYOYO-1 bound to DNA. In some aspects, the biopolymer molecules beingmoved and photocleaved may comprise DNA or RNA.

In some aspects, the method also includes labeling the biopolymermolecules with an indicator or photon absorber to facilitatephotocleavage of the biopolymer molecules when exposed to the lightsource. In some aspects, the light source may be configured to generatelight matched to the indicator or photon absorber used to label thebiopolymer molecules so as to maximize photocleavage of the biopolymermolecules when exposed to the light. In some aspects, the indicator usedto label the biopolymer molecules may comprise one of YO, YOYO-1,YOYO-3, TOTO, methylene blue, Cu or Rh, compounds useful forphotodynamic therapy, or any other photon absorber capable offacilitating photocleavage of the biopolymer. Each indicator can beexcited with a specific wavelength or a range of wavelengths to inducephotocleavage in an efficient manner. In some aspects, the method mayfurther comprise detecting a clogged or reduced flow condition. In someaspects, the detecting comprises identifying that a transport of thebiopolymer molecules through the device falls below a thresholdtransport value. In some aspect, the detecting comprises direct imagingof at least one fluidic channel in or on the device to indicateclogging. In some aspects, the cleaning of the region of the device inwhich the clogging has occurred is implemented in an automatic fashionat one of a predetermined time or a predetermined transport threshold.In some aspects, the method may further include positioning the lightsource in a manner effective to minimize exposure of the device to thelight source.

Another aspect disclosed is an apparatus for enhancing fluid flow. Insome aspects, the apparatus may include a light source configured togenerate light configured to photocleave biopolymer molecules and acontroller configured to control a movement of the biopolymer moleculesinto contact with at least one fluidic channel in or on a device,whereby clogging occurs in the device due to coiling or aggregation ofthe biopolymer molecules or adsorption to or tangling around thechannels or other nano- or micro-patterned features inside the channelor fluidic device, direct the light source at a region of a device inwhich a clog of biopolymer molecules has formed, and activate the lightsource to generate the light beam for an amount of time to facilitate aphotocleaving of the biopolymer molecules forming said clog.

In some other aspects, the apparatus further comprises a motive forcegenerator configured to generate a motive force, wherein the controlleris configured to control a movement of the biopolymer molecules via thegenerated motive force and wherein the controller is further configuredto apply the motive force to fluid in the region of the device in whichsaid clog occurred in a manner effective to flush the photocleavedbiopolymer molecules from the region. In some other aspects, the motiveforce of the apparatus comprises at least one of an electrostatic force,a pneumatic force, a capillary force, or any combination thereof. Insome aspects, the motive force generator is configured to generate oneof an electrostatic force, a pneumatic force, a capillary force, or anycombination thereof. In some aspects, the light beam generated by thelight source may have a wavelength of one of about 473 nm or 488 nm. Insome other aspects, wherein the biopolymer molecules or the apparatusmay comprise DNA or RNA.

In some other aspects, the apparatus may further comprise a biopolymermolecule labeling device configured to label the biopolymer moleculeswith an indicator or photon absorber to facilitate photocleavage of thebiopolymer molecules when exposed to the light beam generated by thelight source. In some aspects, the indicator used to label thebiopolymer molecules comprises at least one of YO, TOTO, methylene blue,Cu or RH, compounds useful for photodynamic therapy, or any othersuitable photon absorber. In some aspects, the apparatus may furthercomprise a detector configured to detect a clog or reduced flowcondition through the at least one fluidic channel in or on the device.In some aspects, the detector may be further configured to identify thata transport of biopolymer molecules through the at least one fluidicchannel in or on the device falls below a threshold transport value. Insome aspects, the detector may be further configured to directly imagethe at least one fluidic channel in or on the device to indicate theclog.

In some other aspects, the controller is further configured to operatethe light source and enhance fluid flow in at automatic fashion at oneof a predetermined time or a predetermined transport threshold. In someother aspects, the apparatus further comprises an x, x-y, or x-y-ztranslation motor configured to position the light source in a mannereffective to minimize exposure of the device to the light source andfurther configured to allow positioning of the light source at anylocation in relation to the device.

In another implementation, light is directed to the region of thefluidic structure for the purposes of photocleavage by bringing alight-source such as an LED into close proximity to the fluidicstructure without use of lenses or other optical systems. Either the LEDor the fluidic structure could be translated into position to accomplishthis. The controller would coordinate movements, light intensity andduration of exposure. A mask in between the light and the fluidicstructure can be used to minimize exposure to regions that should not besubject to photocleavage or degradation, such as the sample wellcontaining molecules that have yet to be loaded into the interrogationregion of the chip.

Another implementation is to include light emitting regions into thefluidic device to apply local excitation and photocleavage to aparticular region of the fluidic device that is subject to blockage orclogging.

Another aspect includes an apparatus for characterizing a biopolymermolecule. The apparatus comprises a fluidic device comprising adetection region comprising at least one channel and the biopolymermolecule. The apparatus further comprises a motive force generator thatmoves biopolymer molecules into the detection region, where a clog ofbiopolymer molecules may occur in the fluidic device and hamper furtherflow of new biopolymer molecules to the detection region. The apparatusfurther comprises a detection system for determining a characteristic ofthe biopolymer molecules in the detection region and a light source setto deliver a light comprising a configuration for photocleaving thebiopolymer molecules forming the clog. The apparatus further comprises alight delivery system to deliver the light to any region of the fluidicdevice and a positioning system to target the detection system to thedetection region for characterization of the biopolymer molecules, andto target the light comprising the photocleaving configuration to aregion of the device where the clog has formed. The apparatus alsocomprises a controller configured to activate the motive force generatorto move the biopolymer molecules into the detection region, direct thedetection system to the detection region, activate the detection systemto determine the characteristics of the biopolymer molecules, direct thelight source configured for photocleaving biopolymer molecules to theregion where the clog has formed, activate the light source to generatea light for photocleaving biopolymer molecules forming the clog, andactivate the motive force generator to flush out the photocleavedbiopolymer molecules; wherein additional new biopolymer molecules flowinto the detection region for characterization.

Another aspect may include a method for characterizing a biopolymer. Themethod may comprise moving biopolymer molecules into a detection regionof a fluidic device, whereby clogging may occur in the device, hamperingfurther flow of biopolymers to the detection region. The method mayfurther comprise detecting a characteristic of the biopolymer moleculesin the detection region. The method may further comprise directing alight source at a region of the device where the clog has formed andphotocleaving the biopolymer molecules causing the clogging. Then, themethod may comprise applying a motive force to flush the photocleavedbiopolymer molecules and applying a motive force to flow additionalbiopolymer molecules for characterization.

Another aspect may include another method for characterizing abiopolymer. The method may comprise moving biopolymer molecules into adetection region of a fluidic device and detecting a characteristic ofthe biopolymer molecules in the detection region. The method may furthercomprise directing a light source at the detection region wherein thelight source comprises a configuration for photocleaving biopolymermolecules. The method further comprises photocleaving biopolymermolecules which have been characterized and flushing photocleavedmolecules, allowing entry of new molecules for characterization.

Another aspect may include a system for characterizing a biopolymer. Thesystem may comprise a fluidic device comprising a detection regioncomprising at least one channel, and further comprising the biopolymerand a detection system for determining a characteristic of thebiopolymer molecule in the detection region. The system may furthercomprise a photo cleaving system comprising a light source set todeliver a light comprising a configuration for photocleaving biopolymermolecules that have already been interrogated or were not interrogatedand do not need to be, for loading new molecules for characterization.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a schematic illustration of a non-limiting embodiment of ananofluidic or microfluidic structure that may be used for biopolymeranalysis.

FIG. 2 depicts an alternate non-limiting embodiment of a nanofluidic ormicrofluidic structure that may be used for biopolymer analysis.

FIG. 3 depicts another non-limiting embodiment of a nanofluidic ormicrofluidic structure that may be used for biopolymer analysis.

FIG. 4 is a block diagram of a non-limiting embodiment of a controlsystem for a system for biopolymer analysis.

FIG. 5 is a flow diagram of a process for cleaning a nanofluidic ormicrofluidic structure after being used to linearize biopolymermolecules.

FIG. 6 is a flowchart of one exemplary method of enhancing fluid flow.In some aspects, the process 600 may be performed by the biopolymermolecule analysis system 400.

DETAILED DESCRIPTION

In the description provided herein, reference is made to theaccompanying drawings, which form a part hereof. The illustrativeembodiments described in the detailed description, drawings, and claimsare not meant to be limiting. Other embodiments may be utilized, andother changes may be made, without departing from the spirit or scope ofthe subject matter presented here. It will be readily understood thatthe aspects of the present disclosure, as generally described herein,and illustrated in the Figures, can be arranged, substituted, combined,and designed in a wide variety of different configurations, all of whichare explicitly contemplated and made part of this disclosure.

It is to be appreciated that certain features of the invention whichare, for clarity, described herein in the context of separateembodiments, may also be provided in combination in a single embodiment.Conversely, various features of the invention that are, for brevity,described in the context of a single embodiment, may also be providedseparately or in any sub-combination. Further, reference to valuesstated in ranges includes each and every value within that range.

Unless defined otherwise, technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs.

As used herein, the term “channel” means a region defined by borders.Such borders may be physical, electrical, chemical, magnetic, and thelike. The term “nanochannel” is used to clarify that certain channelsare considered nanoscale in certain dimensions; similarly, the term“microchannel” is used to clarify that certain channels are consideredmicroscale in certain dimensions. Also as used herein, nanofluidic maymean a fluid system having components whose dimensions are on thenanoscale, while microfluidic may mean a fluid system having componentswhose dimensions are on the microscale. As used herein, biopolymeranalysis may refer to analysis of a macromolecule or biopolymer, such asDNA or RNA, using a nanoscale structure, such as a nanochannel, e.g., ananofluidic system, and microanalysis may refer to analysis of amacromolecule or biopolymer, such as DNA or RNA, using a microscalestructure, such a microchannel, e.g., a microfluidic system. In someembodiments, biopolymer analysis may comprise biopolymercharacterization, wherein a characteristic of the biopolymer moleculemay include a physical dimension (i.e. length, width, etc.), a landmarkperiodicity, shape, enumerating molecules, size, density, electricalproperty, light scattering/refraction, etc.

As used herein, the term “nanochannel” may also refer to “microchannel.”Thus, a device, system, or method that utilizes a nanochannel may beinferred to also apply to or be capable of utilizing a microchannel.Furthermore, any term utilizing the prefix “nano” may be replaced withthe prefix “micro.” For example, discussions of “nanochannels” or“nanofluidic” include “microchannels” and “microfluidic.”

As used herein, the term “DNA” refers to DNA of any length (e.g., 0.1 Kbto 100 megabase). The DNA can be a highly pure preparation, crude, orsemi crude material. The DNA can come from any biological source or canbe synthetic.

As used herein, a “sample” may include any fluid containing a biopolymerthat can be introduced into a microfluidic or nanofluidic device. Thesample may include any fluid that contains a biopolymer of interest, forexample purified and labeled DNA to be analyzed for optical genomemapping or sequencing. In some embodiments, the sample may be highlyprocessed fluid that is applied to the nano- or microfluidic chip foranalysis (i.e., an analyte). The sample can contain buffers andadditives to modify the surface of the fluidic device to facilitateelectrophoresis or prevent adsorption. In some embodiments, the samplecan, for example, include one or more components of blood, serum,plasma, sputum, lavage fluid, cerebrospinal fluid, tissue,microorganisms, urine, semen, sweat, tears, saliva, and the like,including any fractions or processed portions thereof. Similarly, wherea sample is taken from a biopsy, swab, smear, etc., the “sample”expressly encompasses a processed fraction or portion derived from thebiopsy, swab, smear, etc. Linearizing biopolymers may be beneficial invarious biopolymer analysis systems. For example, linearization may beused in systems that image biopolymers, biopolymer optical mappingsystems, sequencing systems, or in biopolymer transfection systems. Suchlinearization may be critical for studying, using, and/or analyzing thephysical and biological properties of the biopolymer molecules. Somebiopolymer analysis systems may use various methods or structures tolinearize the biopolymers. In some embodiments, the biopolymer analysissystem may include a fluidic device having a detection region, while insome embodiments, the biopolymer analysis system may include anapparatus having the fluidic device. The detection region may compriseat least one channel (e.g., a nanofluidic or microfluidic channel)through which the biopolymer flow. In some embodiments, the fluidicdevice may be a disposable, detachable unit (i.e., a chip as describedbelow), a detachable, reusable unit, or a permanent or detachable partof the biopolymer analysis system or apparatus. For example, the fluidicdevice may be a Mapcard or similar unit. The detection region maycomprise one or more fluidic channels (e.g., nano- or microfluidicchannels). For example, some systems may utilize a tapered region tofacilitate linearization and to introduce biopolymers into fluidicchannels. Others may use a variety of obstacles or pillar regions orarrays through which the biopolymer molecules are fed via a motiveforce, the pillar regions or arrays causing the biopolymer molecules tostraighten as they move through and around the pillars. Other systemsmay use confinement in nano- or microchannels, may feed the biopolymermolecules through nanoslits, nanopores, microslits, or micropores, ormay insert the biopolymer molecules within reconfigurabletunable/elastomeric channels to linearize the biopolymers. Some may useopen-topped channels on a surface of a substrate. Some systems mayutilize other linearization methods or combinations of linearizationmethods and structures to linearize biopolymers. In the discussionbelow, various embodiments may be described. One of ordinary skill inthe art would understand that these embodiments are a subset of theexamples of fluidic systems in which biopolymers are directed and arenot intended to be limiting except as specifically called out in claims.

For example, in a system for linearizing biopolymer molecules,nanochannels (or microchannels) can be used to straighten or transportthe biopolymer molecules (e.g., DNA molecules) or maintain them in alinearized form to allow for imaging, mapping and/or sequencing of thebiopolymer molecule. Such channels may be formed on or in nanofluidic(or microfluidic) chips or similar structures that may be easilyreplaceable or removable from a biopolymer analysis system or may bepermanent fixtures of a biopolymer analysis system. In some embodiments,the nanofluidic or microfluidic structures may comprise one or more ofthe linearizing systems or methods discussed above. In otherembodiments, the nanofluidic or microfluidic structures may comprise thelinearizing systems or methods above and additional structures used bythe biopolymer analysis system, e.g., a sample well or reservoir. Thenanofluidic or microfluidic structures may comprise a plurality or anarray of the nanochannels (or microchannels) therein that are used totranslocate or straighten the biopolymers. High efficiency and highthroughput imaging devices may have a large number of parallel arrays ofnanochannels used for the linearization process, e.g., 10, 50, 100, 500,1000, 5000 or more nanochannels in an array. In operation, thebiopolymer analysis system may be repeatedly loaded with biopolymermolecules, and the biopolymer molecules may be directed to flow throughthe biopolymer analysis system (e.g., the fluidic device) under a motiveforce, e.g., an electrokinetic force, pneumatic force, a capillaryforce, or any combination thereof, to move the biopolymer molecules intothe detection region. For example, flow of biopolymer molecules, througha biopolymer analysis imaging system may comprise flow through one ormore linearization regions and the plurality of nanochannels maycomprise an imaging region, where the biopolymer molecules, now havingbeen linearized, may be effectively and efficiently imaged using imagingdevices. In the biopolymer analysis system, a motive force, e.g., fluidpressure or an electric field, may be used to drive the biopolymermolecules through the system.

Further, the biopolymer analysis system or apparatus therein maycomprise a detection system configured to determine a characteristic ofthe biopolymer molecules in the detection region of the fluidic device.In some embodiments, the detection system may comprise anoptically-based device configured to use fluorescence to interrogate thebiopolymer molecules. In some embodiments, the detection system may bean electrochemical detection system configured to operate independentlyof or in conjunction with the optically-based detection system (forexample, for defining stretched biopolymer molecules). In someembodiments, the optically-based device configured to use fluorescenceto interrogate the biopolymer molecules may use a same light source usedfor interrogation for photocleaving purposes. For example, when beingused for photocleaving as opposed to interrogation, the light source maybe tuned up (as is the case with the blue laser, 473 or 488 nm, used forbackbone DNA detection and photocleaving. In some embodiments, theamount of energy required for photocleaving may be 10 to 100 timesgreater than the energy required for imaging. However, one or moreoptical detection components used for biopolymer molecule imaging (e.g.,the CCD or CMOS camera) may not be used for biopolymer photocleavage.

The biopolymer analysis system may further comprise a motive forcegenerator and a detection system, the detection system configured todetermine a characteristic of the biopolymer molecules in the detectionregion. The light source described above may be configured to deliver alight comprising a configuration for interrogating biopolymer moleculesor photocleaving biopolymer molecules forming a clog in the fluidicdevice. In some embodiments, the light source may comprise one or morelasers with a specific or adjustable wavelength, an LED/OLED, anincandescent lamp, a mercury lamp, a UV lamp, an arc lamp, an argonlamp, or any other gas lamp (e.g., neon and krypton). The light sourcecan be pulsating (i.e., turned on for a finite amount of time in bursts)or continuous, gated by physical shutters, filtered, amplified,dampened, polarized, or otherwise manipulated to generate a light usedto interrogate biopolymer molecules at a variety of differentwavelengths and intensities.

In some embodiments, the energy used for photocleavage may bedestructive to multiple species of label. For example, labels that arered-shifted in emission, such as Cy3 or Atto 532, may be destroyed ordamaged by a 488 nm light source used to photocleave biopolymermolecules labeled with YOYO-1. Thus, the use of photocleavage processesand energies may inhibit subsequent attempts to image such biopolymermolecules that have been photocleaved, and care must be used to ensurethe photocleavage has minimal effects on non-targeted biopolymermolecules and labels. In some embodiments, matching of the lightgenerated by the light source to the label to be photocleaved may reducethe destructive effects of the light on non-targeted species of label.Additionally, in an optical detection system using fluorescence,additional wavelengths may be used for target multiplexing (targetsbeing landmarks within a molecule, i.e. a defined sequence in a DNA), orsample multiplexing (different samples labeled with different colors orcolor combinations).

In some embodiments, the optically-based detection system may furthercomprise mirrors, objectives, lenses, filters, shutters, fiber opticcable, or any combination thereof. The optically-based detection systemmay further comprise a focusing mechanism to ensure maximum photondelivery for photocleaving (where the light source of the detectionsystem is used for photocleaving and interrogating) and to provide tightfocus for maximum clarity when interrogating biopolymers.

In some embodiments, a light delivery system may be configured todeliver the light generated by the light source to any region of thefluidic device. The light delivery system may comprise an opticalsystem, or close proximity based delivery system bypassing the opticalsystem, or a combination of the two, wherein DNA detection andinterrogation of biopolymer molecules may occur via the optical systemand photocleaving may occur by direct irradiation while protectingbiopolymer molecules outside the interrogation zone.

The biopolymer analysis system may further include a positioning systemand a controller, wherein the positioning system may be configured totarget the detection system to the detection region for characterizationof biopolymer molecules and to target a photocleaving light to a regionof the fluidic device where the clog has formed. In some embodiments,the positioning system may be capable of movement in one or more of thex-, y-, and z-directions. In some embodiments, the positioning systemmay include a lag-screw based motion system or a piezo or stick-slipmotion system. In some embodiments, the positioning system may includean internal or external encoder or another feedback mechanism to achieveaccurate positioning.

In some embodiments, a controller may be configured to activate themotive force generator to move biopolymer molecules into the detectionregion and to direct the detection system to the detection region. Thecontroller may be further configured to activate the detection system todetermine characteristics of the biopolymer molecules. When a clog hasformed in the fluidic device, the controller may direct the light sourceconfigured for photocleaving biopolymer molecules to the region wherethe clog has formed and activate the light source to generate a lightfor photocleaving biopolymer molecules forming the clog. Thereafter, thecontroller may activate the motive force generator to flush out thephotocleaved biopolymer molecules so that additional new molecules canflow into the detection region for characterization.

FIG. 1 depicts an embodiment of a nanofluidic or microfluidic structure100 that may be used in a biopolymer fluidic system. The components ofan embodiment of the nanofluidic or microfluidic structure 100 aredepicted. The nanofluidic or microfluidic structure 100 is adjacent to asample well 120 or other sample source, such as a larger fluidicchannel. The sample well 120 may be filled with a liquid samplecontaining a biopolymer or macromolecule, for example DNA molecules 152.The fluid sample can also contain buffer for purposes of electrophoresisand surfactants and other additives for surface modification. Themovement of DNA molecules 152 through the nanofluidic or microfluidicstructure 100 is described herein as an example, and embodiments of thepresent disclosure are not limited thereto. While the biopolymers ormacromolecules described herein are exemplified by DNA molecules 152,one of skill in the art will understand this is merely an example of abiopolymer and not limiting.

The nanofluidic or microfluidic structure 100 may be divided intovarious zones, such as a transition zone 150 a and a nanochannel zone150 b. The transition zone 150 a can include a lip region 151, one ormore feeder channels 153, a pillar or deconvolution or linearizingregion 154, and one or more relaxation channels 157. The lip region 151is advantageously adjacent to a sample well 120 and may comprise araised portion with respect to the sample well 120. The lip region 151can be the first part of the nanofluidic or microfluidic structure 100that the DNA molecule 152 encounters when being moved, translocated, orotherwise driven from the sample well 120 using, for example,electrophoresis. The lip region 151 provides a transition area for DNAmolecules 152 leaving the sample well 120 and entering the subsequentregions of the nanofluidic or microfluidic structure 100. A coiled orentangled DNA molecule 152 is depicted in the lip region 151, havingbeen driven from the sample well 120. The lip region 151 may have adepth of from about 0.1 microns to about 10 microns, as measured from atop surface of the well structure 124. The lip region may be from about0.5 micron to about 1000 microns in length, wherein length is defined asbeing in the direction transversing the nanofluidic or microfluidicstructure 100 from one sample well 120 to another. In some embodiments,the lip region is about 1.5 microns deep and about 15 microns in length.The dimensions provided herein are exemplary only, and the dimension maybe construed to be any value within the listed ranges.

Adjacent to the lip region 151 are the one or more feeder channels 153.The feeder channels 153 funnel or direct the coiled or entangled DNAmolecules 152 into a pillar region 154. The one or more feeder channels153 run parallel to each other, and are wide channels, relative to thenanochannels 128. The feeder channels 153 may have a width of about 0.05microns to about 25 microns, or any value therebetween, wherein width isunderstood to be in a direction perpendicular to length as describedabove. The feeder channels 153 may have a depth of from about 20 nm toabout 1000 nm, or any value therebetween. In some embodiments, thefeeder channel is about 50 nm in depth and about 1.5 microns wide.

In one embodiment, the feeder channels 153 may lead to the pillar region154. The pillar region 154 includes a floor 156 which, in someembodiments, is contiguous with the bottom surface of the feederchannels 153. The pillar region 154 also includes one or more pillars155. The pillars 155 may be silicon formations which are interspersedthroughout the pillar region, with the pillars 155 extending from thefloor 156 of the pillar region to a top portion which is raised abovethe floor 156. In some embodiments, the top portion of the pillar regionis in the same plane as the top surface of the well structure 124, andmay be in contact with the substrate (not shown). The pillars 155 may beof any shape, that is, the pillars may have a cross-sectional shapewhich is round, square, diamond, ovoid, rectangular, or any otherdesired shape. The pillars 155 may vary from one to another in size,shape, height, and distance from other pillars 155. The pillars 155 maybe evenly spaced or unevenly spaced throughout the pillar region 154. Insome embodiments, the pillar region 154 may include multiple zones(e.g., two or more zones) of pillars 155, wherein a first zone comprisespillars of one a first dimension, shape, and/or height, and a secondzone of pillars comprises pillars 155 of a second dimension, shape,and/or height, different from the first dimension. In one embodiment,the pillars 155 vary from larger to smaller dimension as they arefurther removed from the feeder channels 153 and closer to thenanochannels 128.

The pillars 155 within the pillar region 154 are sized, shaped, andpositioned to untangle, uncoil, or otherwise straighten tangled orcoiled biopolymers or macromolecules. For example, the size of thepillars 155 and the spacing between the pillars 155 creates a tortuousflow path through which the coiled or tangled DNA molecule 152 cannotfit. Thus, as a motive force, such as an electrostatic field, is appliedacross the nanofluidic or microfluidic structure 100, the coiled ortangled DNA molecule 152 is mechanically forced to uncoil as themolecule interacts with the pillars 155. As shown, there may be morethan one zone of pillars 155, and the pillars 155 of the different zonesmay have different properties. For example, in some embodiments, thespacing between the pillars 155 of the first zone may be larger than thespacing of the pillars 155 of the second zone. In this way, the firstzone causes an initial partial untangling or uncoiling, before themolecules reach the second zone. In the second zone, the molecules areforced through narrower spaces, which can cause a further untangling oruncoiling of the molecules. The distance between pillars 155 can vary.For example, the distance between two pillars 155 can be about 25 nm,about 50 nm, about 100 nm, about 150 nm, about 200 nm, about 250 nm,about 300 nm, about 350 nm, about 400 nm, about 450 nm, about 500 nm,about 1000 nm, about 2000 nm, about 3000 nm, about 4000 nm, about 5000nm, or a range between any two of these values. In some embodiments, thedistance between pillars 155 is about 0.1 micron to about 2.5 microns.

The pillars 155 may have a height, that is, a distance from the floor156 to their top surfaces of from about 20 nm to about 5000 nm, or anyvalue therebetween. In some embodiments, the pillars 155 may have awidth, diameter, or long dimension, depending on their shape, of fromabout 50 nm to about 10000 nm, or any value therebetween. In someembodiments, the pillars 155 have a height of about 50 nm and a width,diameter, or long dimension, of from about 200 nm to about 5000 nm. Asshown, the pillars 155 of the different zones may be of differentdiameters, where the pillars 155 of the first zone may have a largerdiameter than the pillars 155 of the second zone. Additionally, thedensity of the pillars 155 in the pillar region 154 may increase aspillar region 154 nears the nanochannel wells 128.

The pillar region 154 adjoins a plurality of relaxation channels 157.The relaxation channels 157 are channels that act as inlets to theplurality of nanochannels 128. In some embodiments, the relaxationchannels 157 are funnel shaped channels. The relaxation channels 157have a wider dimension at an end adjacent to the pillar region 154 and anarrower dimension at an end proximate to the nanochannels 128. Therelaxation channels 157 receive uncoiled and untangled or partiallyuncoiled and untangled molecules and help to further linearize themolecules as the molecules enter the plurality of nanochannels 128. Alinearized DNA molecule 158 is depicted entering one nanochannel 128from the associated relaxation channel 157. The relaxation channels 157may be from about 10 to about 5000 microns long, about 20 nm to 300 nmdeep, and about 50-1000 nm wide. In some embodiments, the relaxationchannels 157 may be about 80 microns long, 50 nm deep, and 300 nm wide,at their widest point.

The plurality of nanochannels 128 receive the linearized DNA molecules,and are sized such that only linearized molecules can fit into and canbe transported or moved through the nanochannels 128. The nanochannels128 may be from about 20 nm to about 300 nm wide, about 30 to about 300nm deep, and from about 10 to about 10000 microns long. In someembodiments, the nanochannels are about 45 nm wide, about 45 nm deep,and about 350 microns long.

During use, it is possible for the nanochannel 128 to become cloggedwith the biopolymer molecule 152 that is being translocated through thenanochannel 128 (see clog 130). The clog may hamper further flow of newbiopolymer molecules through the nanochannel 128 and/or the fluidicdevice. In other instances, the nanochannel 128 may be clogged wherethey meet with the relaxation channel 157 (see clog 132) or therelaxation channels 157 may become clogged or blocked by DNA molecules112 that do not fully uncoil through the pillar region 154 or thatre-coil once they pass through the pillar region 154 (see clog 134).Alternatively, the pillar region 154 may become clogged by DNA molecules152 that do not properly uncoil or that wrap around one or more pillars155 and accumulate (see clog 136). Additionally, a clog 138 may formwhere the sample well 120 meets the feeder channels 153.

In a more general sense, as applied to fluidic devices in general, DNAor other biopolymer may accumulate or clog in any region of fluid flow,but more usually in branch points, valves, transitions from larger tosmaller channels, points where turbulent flow occurs, entrances tochannels smaller than the dimension of coiled biopolymer, wastechannels, flow passages of low velocity, regions where flow is stoppedfor a period of time, or areas where biopolymer may aggregate orprecipitate or become adsorbed upon or entangled with any surface of thefluidic device including pillars, sidewalls of the nanochannels, or anyother linearization structure.

FIG. 2 depicts an alternate embodiment of a nanofluidic or microfluidicstructure 200 that may be used for biopolymer analysis. The componentsof an embodiment of this nanofluidic or microfluidic structure 200 aredepicted and may be similar to those described in relation to FIG. 1.The nanochannel 228 is shown adjacent to a sample well 220. In someembodiments, both the nanochannel 228 and the sample well 220 may bepart of the nanofluidic or microfluidic structure 200. In otherembodiments, only the nanochannels 228 may be part of the nanofluidic ormicrofluidic structure 200. The sample well 220 may be filled with aliquid sample containing a biopolymer or macromolecule, for example DNAmolecule 252. The liquid sample can also contain buffer for purposes ofelectrophoresis and surfactants and other additives for surfacemodification. The movement of DNA molecules 252 through the nanochannelstructure 200 is described herein as an example, and embodiments of thepresent disclosure are not limited thereto. While the biopolymer ormacromolecule described herein are described as DNA molecules 252, oneof skill in the art will understand this is merely an example of abiopolymer and is not limiting.

Coiled or entangled DNA molecule 252 is depicted in the sample well 220.Adjacent to the sample well 220 are the plurality of nanochannels 228.The plurality of nanochannels runs parallel to each other. The pluralityof nanochannels 228 receive the linearized DNA molecules and may besized such that only significantly linearized molecules can fit into andcan be transported or moved through the nanochannels 228. Thenanochannels 228 may advantageously be from about 20 nm to about 300 nmwide, about 30 to about 300 nm deep, and from about 10 to about 10000microns long. In some embodiments, the nanochannels 228 are about 45 nmwide, about 45 nm deep, and about 350 microns long. As depicted, one ormore DNA molecules 252 may be located in one of the one or more samplewells 220 and/or the plurality of nanochannels 228. In some embodiments,the DNA molecules 252 may be located in both a sample well 220 and ananochannel 228 at the same time.

The size and the spacing of the nanochannels 228 may create arestrictive flow path through which the coiled or tangled DNA molecule252 cannot fit. Thus, as the motive force, such as an electric field, isapplied across the nanofluidic or microfluidic structure 200, the coiledor tangled DNA molecule 252 is mechanically forced to uncoil as themolecule interacts with the nanochannels 228 from the sample well 220.

During use, it is possible for the nanochannel 228 to become cloggedwith the biopolymer molecule 252 that is being translocated through thenanochannel 228 (see clog 230). Alternatively, the point where thesample well 220 and the nanochannels 228 meet may become clogged orblocked by coiled DNA molecules 228 that do not properly uncoil underthe motive force as they should to move into the nanochannel 228 (seeclog 232).

FIG. 3 depicts another embodiment of a nanofluidic or microfluidicstructure 300 that may be used for biopolymer analysis. The componentsof an embodiment of this nanofluidic or microfluidic structure 300 aredepicted and may be similar to those described in relation to FIG. 1. Insome embodiments, the nanofluidic or microfluidic structure 300 maycomprise a nanochannel 328 and a sample well (not shown). In otherembodiments, only the nanochannels 328 may be part of the nanofluidic ormicrofluidic structure 300. The sample well may be filled with a liquidsample containing a biopolymer or macromolecule, for example DNAmolecule 352. The liquid sample can also contain buffer for purposes ofelectrophoresis and surfactants and other additives for surfacemodification. The movement of DNA molecules 352 through the nanochannelstructure 300 is described herein as an example, and embodiments of thepresent disclosure are not limited thereto. Nanoslits 324 may existbetween each of the nanochannels 328. As depicted, the nanoslits 324 mayrun diagonally between two nanochannels 328. The nanoslits 324 may workto linearize the DNA molecules 352 when the nanochannels 328 are loadedwith the DNA molecules 352 and the DNA molecules 352 pass through thenanoslits 324. As depicted, one or more DNA molecules 352 may be locatedin one of the one or more nanochannels 328 and/or one or more nanoslits324. In some embodiments, the DNA molecules 352 may be located in both asample well, a nanochannel 328, and a nanoslit 324. While the biopolymeror macromolecule described herein are described as DNA molecules 352,one of skill in the art will understand this is merely an example of abiopolymer and is not limiting.

A coiled or entangled DNA molecule 352 is depicted in the one or morenanochannels 328. The plurality of nanochannels runs parallel to eachother. The nanochannels 328 may be from about 20 nm to about 300 nmwide, about 30 to about 300 nm deep, and from about 10 to about 10000microns long and may receive linearized or coiled DNA molecules 352. Insome embodiments, the nanochannels 328 are about 100 nm wide, about 100nm deep, and about 350 microns long. In some embodiments, the nanoslits324 are about 45 nm wide, about 45 nm deep, and about 45 microns long.In some embodiments, the DNA molecules 352 may be located in both asample well and a nanochannel 328 at the same time. A linearized DNAmolecule 358 is depicted flowing through one nanoslit 324.

The nanofluidic or microfluidic structure 300 may be used to translocateat least a portion of a biopolymer molecule from the sample wellsthrough the nanochannel 328. However, during use, it is possible for thenanochannel 328 to become clogged with the DNA molecule 352 that isbeing translocated through the nanochannel 328 (see clog 330).Alternatively, the region where the sample wells and the nanochannel 328meet may become clogged or blocked by coiled or accumulated DNAmolecules 352 (see clog 332). Additionally, the nanoslits 324 may becomeclogged or blocked by DNA molecules 352 (see clog 334).

Once clogged, the efficiency of the linearization process using theclogged nanofluidic or microfluidic structures may decrease. Also, onceclogged it can be difficult to introduce fresh biopolymer molecules intothe nanofluidic or microfluidic device and manipulate them therein,seriously limiting throughput and utility. Clogging can further changethe optimal electrical conditions required to manipulate biopolymermolecules in the nanofluidic or microfluidic structure, resulting insubpar throughput. Heterogeneous clogging throughout a plurality ofnanochannels can give rise to heterogeneous response to electric fieldsfrom one portion of the microfluidic or nanofluidic device to the next.The rate of clogging can increase when existing biopolymer molecules areclogged inside the nanofluidic or microfluidic device, creating asnowball effect that accelerates clogging. Given the size of thenanochannels of the nanofluidic or microfluidic structure, clearing thechannels through physical or similar means (e.g., cleaning solutions orphysical cleaning devices) may be difficult and/or impractical.

Nanofluidic or microfluidic structures, including but not limited tothose depicted in FIGS. 1-3 may initially achieve a high throughput whenloading the biopolymer molecules into the nanochannel or microchannelregion. As the linearization region and nanochannels are repeatedly usedfor linearizing more biopolymer molecules, the linearization region andnanochannels may become clogged with tangled or accumulated biopolymermolecules. Similarly, the nanochannels may become clogged by moleculesthat are not completely linearized when they enter into the nanochannelsor when multiple molecules enter a nanochannel at one time. Suchtangling and/or clogging can cause reduced throughput as the cloggedportions inhibit the ability for the DNA molecules to flow through thedesired flow passages, such as nanochannels. For example, over time,when driving DNA through an array of nanochannels, more and morenanochannels will become clogged, so fewer channels can be used toprovide information. The reduced number of DNA molecules travelingthrough the nanochannels results in reduced throughput or reducedinformation density in the array. Other fluidic devices can similarlybecome clogged with DNA or other biopolymers, reducing their utility ina related manner.

Accordingly, the clogged portion of the nanofluidic or microfluidicstructure may need to be cleaned to restore the throughput of the chipsor other structures. As an example, with reference to the structure ofFIG. 1, one method for clearing out the pillar region and thenanochannels may comprise using a laser or other illumination source tochop the biopolymer molecules that are clogging portions of thenanofluidic or microfluidic structure into fine pieces, after whichthose pieces of the chopped biopolymer molecules may be flushed from thenanofluidic or microfluidic structure via an appropriate motive force,such as by electrophoretic force or fluid pressure differential. In someembodiments, the biopolymer molecules may be “YoYo-1” stained or labeledbiopolymer molecules. In some other embodiments, the biopolymermolecules being chopped/photocleaved may be stained or labeled withanother indicator or exposed to another compound (i.e., YO, TOTO,methylene blue, Cu or Rh, compounds for photodynamic therapy, etc.) thatabsorb photons to facilitate or aid photocleavage of the biopolymermolecules when exposed to an illumination source. Thus, photocleavagemay be achieved with or without a stain, label, indicator, or otherphoton absorber. Alternate embodiments may utilize non-stainedmolecules. In some embodiments, the illumination source may be a laser,for example a 473 nm blue laser or a 488 nm laser, or a laser of anyother wavelength. Other embodiments may utilize light energy sources ofother wavelengths, e.g. UV light, and light energy from other sources,e.g. a light-emitting diode. Thus, laser or other light that matches oroverlaps an absorption wavelength of a dye or other absorbing moleculeon the biomolecule can be used to cleave a labeled polynucleotide orother biomolecule, and UV or other high-energy illumination sources canbe used to cleave even unlabeled polynucleotide or other biomolecule.

By applying a dose of laser or other light energy to the nanofluidic ormicrofluidic structure at desired times or intervals, cloggingbiopolymer molecules or stained/labeled biopolymer molecules that canabsorb or be cleaved by the light may be fragmented, and more easilyflushed from the structure. In one embodiment, specific times in arepetitive fluidic process, such as interleaved loading and imagingcycles in an analysis device, may be defined as the times when cloggingbiopolymers should be removed. Alternatively, the amount of clogging canbe at least partially ascertained by detecting reduction of throughputor channels containing biomolecule beyond a threshold amount.Alternatively, direct imaging of the chip can indicate clogging.Alternatively, cleaning can be initiated during times when thenanofluidic or microfluidic structures are not currently being used forlinearization.

For example, with reference to the structure of FIG. 1, the device maydetect or measure the throughput or loading density of the downstreamnanochannels when the pillar regions of the nanofluidic or microfluidicstructure are new and entirely unclogged. The system may be configuredto detect clogging in the nanofluidic or microfluidic structure. Theclog may be detected by identifying a reduced throughput or loadingdensity in the nanochannels. Some embodiments may comprise additionaldetection methods to determine where the clog is located within ananofluidic or microfluidic structure. Once the specific location of theclog is determined, the system may focus the illumination source at thatlocation to focus the dosing energy only where needed and not wastingenergy by unnecessarily dosing portions of the biopolymer analysissystem that are not clogged. Alternatively, the system may directillumination energy effective to fragment clogging biopolymers at leastinto any or all regions of the fluidic device that are susceptible toclogging.

In one embodiment, an initial throughput or loading value in a new orunclogged fluidic device may be determined to be a baseline throughputof the nanofluidic or microfluidic structure and may be the basis fordetermining a threshold level at which point the nanofluidic ormicrofluidic structures are to be cleaned. In some embodiments, thethreshold level may be set as 50% of throughput, such that when thethroughput of the downstream nanochannels falls below 50%, the devicecleans the pillar regions of the nanofluidic or microfluidic structures.In another embodiment, the threshold level may be set at 75% ofthroughput or 25% of throughput, or any value in between these values,or at any other desired threshold, dependent on the requirements for thenanochannel throughput and the ability to clean the pillar region withan appropriate dose of biopolymer-cleaving energy (i.e., the device mayhave an automated ability to apply the photo-energy dose more or lessfrequently). Alternatively, the nanofluidic or microfluidic structuremay be dosed after every loading cycle to ensure the structure is asclear as possible. In any of the embodiments of cleaning describedherein, the cleaning process may be implemented in an automatic fashion,including at a predetermined time or at a predetermined clogging,throughput, or loading value.

FIG. 4 depicts one exemplary embodiment of a control system 400 for abiopolymer analysis system that may automatically or manually performthe method disclosed in FIG. 5. A control system 400 includes acontroller 462 and a memory 464. The controller 462 is in communicationwith the memory 464. The controller may comprise a processor and aninternal memory or cache. The memory 464 may contain computer-readableinstructions for operating the controller 462 and/or the control system400.

The controller 462 is also advantageously in communication with theillumination source(s) 460, one or more x, x-y, or x-y-z translationmotors 492, and a motive force generator 494. The controller 462 isconfigured to power on or off the illumination source(s) 460 and mayalso control the intensity of the illumination source(s) 460 and/or theduration of illumination. In some embodiments, the illuminationsource(s) 460 may provide control of the wavelength of light to beemitted, or may be selected to have strong or peak emissions at adesired wavelength, such as a wavelength at which a biopolymer or labeleffectively absorbs photons in a manner sufficient to effect cleavage.The controller 462 may be configured to control the direction, focus, orwavelength of the illumination beam by controlling the illuminationoptics 470. The illumination source(s) 460 and the illumination optics470, individually or in combination, may advantageously comprise, forexample, a laser light energy source or an LED light energy source, orany other source of photons effective to photocleave the biopolymer inquestion.

The controller 462 is configured to send control signals to one or morex, x-y, x-y-z translation motors 492, such as are described herein. Forexample, the controller 462 may be configured to control operation ofthe x, x-y, or x-y-z translation motor 492 in order to move thenanofluidic or microfluidic structures discussed above to bring portionsof the nanofluidic or microfluidic structure into range/view of theillumination optics 470 and illumination source(s) 460, as needed ordesired. Alternatively, the x, x-y, or x-y-z translation motor 492 maymove the illumination optics 470 and/or the illumination source(s) 460to direct light energy to a specific region or portion of thenanofluidic or microfluidic structure that is clogged or is otherwise isdesired to be cleaned. It should be noted that prophylactic orpreventative cleaning is also contemplated, so that accumulatedbiopolymer can be removed even if no decrease or only minor decrease inperformance has occurred. In some embodiments, the photocleavingcleaning method described herein may be used prophylactically to preventclogging, or may be used in conjunction with other prophylactic cleaningmethods. In some embodiments, the translation motor 492 may be replacedwith the positioning system described above. The controller 462 can beconfigured to operate or supply control signals to the motive forcegenerator 494. The motive force generator may comprise electrodes,pressure generating elements, or other components configured to generatea motive force as described herein. The motive force, as describedabove, may be configured to move the biopolymer molecules through thefluidic device and into the detection region.

In some embodiments, the controller 462 operates by automaticallycontrolling and coordinating the timing of operating the illuminationsource(s) 460, the motive force generator 494, the illumination optics470, and the other portions of the control system 400. For example, insome embodiments, the controller 462 can supply a signal to the motiveforce generator 494 to induce movement of biopolymers or macromoleculesin a fluidic system. After an amount of time has passed, the controller462 may remove the signal, or may provide an interrupt signal to stopapplication of the motive force from the motive force generator 494.After the motive force is removed, the controller 462 may provide asignal to the illumination source(s) 460 to illuminate a portion of thenanofluidic or microfluidic structure which may be clogged withbiopolymers or macromolecules or may otherwise be desired to be cleaned.In some embodiments, the controller 462 may determine that thenanofluidic or microfluidic structure of the biopolymer analysis systemneeds to be cleaned. As discussed above, this determination may be basedon the flow rate of the biopolymers through the nanofluidic ormicrofluidic structure. In other embodiments, the controller 462 mayclean the nanofluidic or microfluidic structure after every sample ofbiopolymers is analyzed by the biopolymer analysis system. Note thatwhile automated systems are disclosed, a manual or partially manualsystem may also be used, if desired. For example, a cleaning cycle couldbe initiated when a user hits a button, makes a menu selection, manuallytranslates the x, x-y, or x-y-z motor to irradiate specific portions ofthe fluidic device, or otherwise initiates a cleaning cycle. This couldoccur whenever a user desires, or can occur, for example, in response toa notification provided by the controller to a user requesting input ifthe user agrees to initiate cleaning.

Cleaning the nanofluidic or microfluidic structure may comprise dosingthe region or portion of the nanofluidic or microfluidic structure to becleared. In one exemplary embodiment, such as when biopolymer moleculessuch as DNA is labeled with a dye or other molecule that absorbs at 473nm, the laser dosing process may involve dosing each biopolymer moleculewith between 1 and 100 MJ/m{circumflex over ( )}2 of 473 nm laser energydensity per cycle depending on the biopolymer molecules that are beinganalyzed with the biopolymer analysis system. For example, in oneembodiment, the most common energy density per cycle may be 15MJ/m{circumflex over ( )}2 of 473 nm laser. Additionally, in otherembodiments, different wavelengths of laser may be used, such as whenDNA is labeled with a different dye or other absorber. A designer canreadily determine an appropriate energy density per cycle that iseffective to photocleave the biopolymer molecules. In this manner,biopolymer molecules that previously clogged a portion of thenanofluidic or microfluidic structure or otherwise clogged, reduced, orinhibited the flow of biopolymer molecules through the fluidic structuremay be cleaved or “chopped” into smaller pieces that can pass from theregions in which such biopolymer molecules have accumulated.

The controller 462 may control the dosing energy of the laser dosingprocess described above by turning on and off the illumination source(s)460 and directing the illumination to the appropriate location using theillumination optics 470. The controller 462 may determine what energydensity should be used based on the biopolymer molecule in each sampleand based on the light energy source being used to photocleave thebiopolymer molecules. For example, as mentioned above, DNA moleculesbeing photocleaved by a 473 nm laser may require 15 MJ/m{circumflex over( )}2 to photocleave when the DNA molecules have been stained with aYoYo-1 fluorescent label. Alternatively, photocleaving DNA moleculesusing UV light may not require staining but may require more energyduring dosing than that of the 473 nm laser. The controller 462 may thusdetermine the amount of time to expose the portion of the nanofluidic ormicrofluidic structure being cleaned to the illumination source(s) 460and the illumination optics 470 and may provide the desired energy levelto the device. Control of the energy level may be achieved by anyappropriate means, such as by pulse width modulation, control of energyinput into the illumination source 460, filtering, or changing theillumination time.

During, or after at least a portion of the fluidic system isilluminated, the controller 462 may signal the motive force generator494 to activate. Activating the motive force generator 494 after thephotocleaving process may flush out the photocleaved fragments of thebiopolymer. After the motive force generator 494 is deactivated, thecontroller 462 may signal the x, x-y, or x-y-z translation motor 492 tomove the nanofluidic or microfluidic structure a specified amount toposition the next portion to be cleaned within range of the illuminationsource(s) 460 and illumination optics 470, or may move the illuminationsource(s) 460 and illumination optics 470 to the appropriate location toclean the next portion of the nanofluidic or microfluidic structure thatneeds to be cleaned. After the nanofluidic or microfluidic structure orthe illumination source(s) 460 and optics 470 have been moved, thecontroller 462 may re-energize the illumination source(s) 460 and optics470 to properly dose the new portion of the nanofluidic or microfluidicstructure and flush the chopped portions of biopolymer molecules toclear the next region of the nanofluidic or microfluidic structure. Thisprocess may repeat as many times as needed to fully clean and clear allclogged portions of the nanofluidic or microfluidic structure, or asdesired. Alternatively some or all of the areas to be cleaned may bescanned with laser or other optical energy one or more times in arepetitive manner until sufficient cleaving energy has beenadministered. This process will be described in more detail with respectto FIG. 5.

FIG. 5 is a flow diagram of an exemplary process for cleaning ananofluidic or microfluidic structure after being used to linearizebiopolymer molecules. A process 500 for cleaning a nanofluidic ormicrofluidic structure may begin at block 502, wherein a samplecontaining an optionally marked, tagged, or stained biopolymer, such asDNA is added to a first reservoir or sample well. In some embodiments, abuffer solution or identical or other liquid or fluid may be added to asecond reservoir or sample well, in order to facilitate theelectrophoresis of the biopolymer or macromolecule. Following additionof the sample, the biopolymer analysis system may form a seal around thereservoir or the nanofluidic or microfluidic structure to preventevaporation of the sample. In some embodiments, the biopolymer analysissystem may include negative and positive electrodes. The negative andpositive electrodes, or portions thereof, may be brought into contactwith the sample in the first reservoir or sample well and the buffersolution or liquid in the second reservoir or sample well, respectively,to provide an electrostatic force to move the biopolymer molecules. Inother embodiments, the motive force may comprise the pressure forcegenerated by the pressure generation element as described above, whichis brought into position after the sample is placed in the reservoir orsample well.

The process moves to block 504, wherein the motive force is applied tothe reservoirs or sample wells. As described above, in some embodiments,this is accomplished by applying an electric field to the sample wellsby using, for example, the negative and positive electrodes, and/or theelectrode portions of the substrate. In some embodiments, this isaccomplished by applying a pressure gradient sufficient to drivemolecules from the first reservoir to the second reservoir through themicrochannels or nanochannels.

The process 500 moves to block 506, wherein the motive force is removedafter a predetermined amount of time. In some embodiments, block 506 maycomprise removing the motive force when the flow through the nanofluidicor microfluidic structure drops below a threshold value, indicating theflow through the nanochannels is complete. Alternatively, the block 506may be timed to allow biopolymers in the nanochannels to move out of thenanochannels and other biopolymers to move into the nanochannels forimaging or other analysis. Upon removal of the motive force in block506, the movement, driving, or migration of molecules through thenanofluidic or microfluidic structure, and, specifically, thenanochannels stops, and the molecules maintain their current positions,either within the nanochannels or in the second reservoir or samplewell. The predetermined amount of time may be determined based on thebiopolymer or macromolecule of interest. In some embodiments, thepredetermined amount of time may be determined based on the quantity ofbiopolymer molecules being linearized and transported by the system. Thetime the motive force is applied may be 1 microsecond, 5 microseconds,10 microseconds, 20 microseconds, 50 microseconds, 0.1 seconds, 0.5seconds, 1 second, 2 seconds, 3 seconds, 4 seconds, 5 seconds, 10seconds, 15 seconds, 20 seconds, 25 seconds, 30 seconds, 45 seconds, 60seconds, 90 seconds, 120 seconds, 5 minutes, 10 minutes, 15 minutes, 20minutes, 30 minutes, or more, or any amount of time therebetween.

The process 500 moves to block 508 wherein either the illuminationoptics or the nanofluidic or microfluidic structure is moved so as todirect illumination for cleaning by a light energy source to be directedonto a desired region of the fluidic structure. For example, if thefluidic structure is to be moved, an assembly or a platform on which thenanofluidic or microfluidic structure is attached may be moved to bringthe nanofluidic or microfluidic structure into position for cleaning. Insome embodiments, for example, a first portion to be cleaned may includethe point where the nanochannels meet the sample well, while a secondportion may include the nanochannels themselves. In some embodiments,the second portion cleaned may include an array of pillars or a subsetof nanochannels, other than those previously cleaned. A person of skillin the art will understand that the second portion of the nanofluidic ormicrofluidic structure cleaned may vary without departing from the scopeof this application.

Alternatively, at block 508, the illumination optics may be moved so asto position the illumination optics to clean a portion of thenanofluidic or microfluidic structure or biopolymer analysis system. Insome of embodiments, the illumination optics may be moved to clean aportion of the nanofluidic or microfluidic structure or biopolymeranalysis system that is immovable. Similarly as described above, theillumination optics may be operated to direct the illumination beam at adifferent portion of the nanofluidic or microfluidic structure or thebiopolymer analysis system, or to scan an area, which can then becleaned using the illumination beam. In some embodiments, for example, afirst portion of the biopolymer analysis system to be cleaned mayinclude nanofluidic or microfluidic structure comprising thenanochannels or an area adjacent to or upstream from an entrance intothe nanochannels. Furthermore, a person of skill in the art willunderstand that any portion of a fluidic system using biopolymers thatcan be exposed to the illumination beam may be cleaned using a similarprocess, adapted as necessary to the particular system in question.Alternatively, an appropriate source of photon energy, such as a UV LEDor visible light LED, or an array or arrangement of such LEDs, may bepermanently positioned to direct photo-cleavage light energy whenactuated onto appropriate portions of a fluidic device.

At block 510, a portion of the nanofluidic or microfluidic structure (orbiopolymer fluidic system) is cleaned. This block may comprise exposinga portion of the fluidic structure to an illumination beam such that anybiopolymer molecules that are remaining in that portion are dosed withenergy from the illumination beam that may react with the biopolymermolecules and photocleave the biopolymer molecules that areappropriately dosed such that the biopolymer is chopped into smallerpieces. As discussed above, the dosing requirements may vary accordingto at least one of the biopolymer molecule, the staining or labelingelement used, or the illumination source being used. In someembodiments, block 510 may be directed to specific locations that aredetermined to need to be cleaned. In some embodiments, block 510 may bedirected to all location of the chip. After photocleaving the selectedregion of the nanofluidic or microfluidic structure, the processproceeds to block 512.

Block 512 may represent an optional dedicated cleaning block that may beinserted after block 510, where the nanofluidic or microfluidicstructure region(s) or the portion of the biopolymer analysis system waspreviously cleaned. The optional block 512 may provide for theapplication of a dedicated motive force to the nanofluidic ormicrofluidic structure or the portion of the biopolymer analysis systemthat has been cleaned by a previous step. The dedicated motive force maybe dedicated to flushing out the chopped pieces of the biopolymermolecules and leaving the area clear of elements that may inhibit theflow of biopolymers through the system. In some embodiments, theprocesses of optional block 512 may be performed after the optionaldecision block 514. In some embodiments, a non-dedicated motive force,such as a motive force used to load the DNA into the chip after aphotocleavage step (e.g., the motive force of Block 504) may be used toclear the chopped pieces of the biopolymer molecules concurrently withthe loading of the next DNA sample.

The process 500 moves to an optional decision state 514 wherein it isdetermined if each portion of the nanofluidic or microfluidic structureor biopolymer analysis system that needed to be cleaned or was scheduledto be cleaned has been cleaned. The portion to be cleaned can include aspecific nanochannel or the full array of nanochannels, or the pillararray (if one exists), or any desired portion of a nanochannel orfluidic device. If the nanofluidic or microfluidic structure orbiopolymer analysis system has not been fully cleaned, the processreturns to step 508, wherein the cleaning of portions of the fluidicstructure or biopolymer analysis system continues.

The process 500 described above may provide an increase in biopolymermolecule loading or throughput through the fluidic system. This increasein loading and throughput may be accomplished without observed sideeffects, such as decreased DNA size, photobleached labels or otherrelated metrics. Additionally, in systems where the cleaning method maybe utilized after every loading instance, the biopolymer analysis systemmay be more aggressively loaded than in a biopolymer analysis systemthat is not cleaned, leading to higher throughput.

A person of skill in the art will understand that the steps of process500 need not be performed in the order specified, nor must all steps beperformed. Furthermore, a person of skill in the art will understandthat the processes may be performed in parallel, and no steps in oneprocess necessarily preclude the performance of steps in anotherprocess. In some embodiments, the processes occur in an overlappingfashion, with steps from one process giving rise to or, initiating stepsfrom another process, or steps from one process being triggered by stepsfrom another process. The process may be fully automatic, may bepartially automated while requiring one or more user inputs, or may bemanually implemented.

FIG. 6 is a flowchart of one exemplary method of enhancing fluid flow.In some aspects, the process 600 may be performed by the control system400. In some aspects, the process 600 may be performed by a standalonephotocleaving system (not shown). Process 600 may demonstrate theprocess of cleaning a nanofluidic or microfluidic structure after beingused to linearize biopolymer molecules, for example the process 500shown in FIG. 5.

At block 605, biopolymer molecules may be moved into contact with atleast one fluidic channel in or on a device, whereby clogging occurs inthe device due to coiling or aggregation of the biopolymer molecules oradsorbtion to or tangling around the channels or other nano- ormicro-patterned features inside the channel or fluidic device. In someaspects, the biopolymer molecules may be moved using a motive force toflush photocleaved biopolymer molecules from the cleaned region. In someaspects, the motive force may comprise an electrostatic, a pneumaticforce, a capillary force, or any combination thereof.

At block 610, the process 600 may direct a light source at a region ofthe device in which said clogging has occurred so as to photocleave anybiopolymer molecules that contribute to said clogging and facilitateremoval or reduction of said clogging. In some embodiments, the lightsource may emit a light having a wavelength of 473 nm or 488 nm. In someaspects, the process 600 may further include labeling the biopolymermolecules with an indicator to facilitate photocleaving of thebiopolymer molecules when exposed to the light source. In some aspects,the block 610 or another block of process 600 (not shown in this figure)may configure the light source to generate light that matches theindicator or photon absorber used to label the biopolymer molecules tomaximize the photocleaving capabilities of the process. Generating lightthat matches the indicator or photon absorber may comprise determiningwhat characteristics of the light (i.e., wavelength, intensity, etc.)would maximize photocleaving of the biopolymer molecules labeled withparticular indicators or photon absorbers. Each indicator or photonabsorber may have a different light (i.e., light with a differentwavelength, intensity, etc.) that maximizes photocleavage of thebiopolymer molecules to which the indicator or photon absorber isapplied. In some aspects, the process 600 may further include detectinga clogged or reduced flow condition prior to or concurrent with or afterthe block 610. In some aspects, the process 600 may be implementedautomatically by system 400 at one of a predetermined time orpredetermined transport threshold. Any of the blocks described above inrelation to process 600 may be performed by one or more of thecomponents of system 400, including the controller 462, the illuminationsource(s) 460 and optics 470, motive force generate 494, and x, x-y, orx-y-z translation motor 492. In some embodiments, one or more of theblocks described above may be performed by components of similarstructure and function as those depicted in FIG. 4.

The technology is operational with numerous other general purpose orspecial purpose computing system environments or configurations.Examples of well-known computing systems, environments, and/orconfigurations that may be suitable for use with the invention include,but are not limited to, personal computers, server computers, hand-heldor laptop devices, multiprocessor systems, processor-based systems,programmable consumer electronics, network PCs, minicomputers,controllers, microcontrollers, mainframe computers, multiple processorsdirectly or indirectly linked, distributed computing environments thatinclude any of the above systems or devices, and the like. Combinationsof these devices can be used together.

As used herein, instructions refer to computer-implemented steps forprocessing information in the system. Instructions can be implemented insoftware, firmware or hardware and include any type of programmed stepundertaken by components of the system.

As used herein, a processor may be any conventional general purposesingle- or multi-chip processor such as a Pentium® processor, a Core 13,15, or 17 processor, a 8051 processor, an AMD FX series processor, aMIPS® processor, an Atom processor, an Alpha® processor, or any otherdesired or suitable processor or combination of processors. In addition,the processor may be any conventional special purpose processor such asa digital signal processor a graphics processor or an embeddedmicrocontroller. The processor typically has conventional address lines,conventional data lines, and one or more conventional control lines.

The system is comprised of various modules as discussed in detail. Ascan be appreciated by one of ordinary skill in the art, each of themodules comprises various sub-routines, procedures, definitionalstatements and macros. Each of the modules are typically separatelycompiled and linked into a single executable program. Therefore, thedescription of each of the modules is used for convenience to describethe functionality of the preferred system. Thus, the processes that areundergone by each of the modules may be arbitrarily redistributed to oneof the other modules, combined together in a single module, or madeavailable in, for example, a shareable dynamic link library.

The system may be used in connection with various operating systems suchas Linux®, UNIX® or Microsoft Windows®.

The system may be written in any conventional programming language suchas C, C++, C#, BASIC, Pascal, or Java, and run under a conventionaloperating system. C, C++, BASIC, Pascal, Java, and FORTRAN are industrystandard programming languages for which many commercial compilers canbe used to create executable code. The system may also be written usinginterpreted languages such as Perl, Python or Ruby.

Those of skill will further appreciate that the various illustrativelogical blocks, modules, circuits, and algorithm steps described inconnection with the embodiments disclosed herein may be implemented aselectronic hardware, computer software, or combinations of both. Toclearly illustrate this interchangeability of hardware and software,various illustrative components, blocks, modules, circuits, and stepshave been described above generally in terms of their functionality.Whether such functionality is implemented as hardware or softwaredepends upon the particular application and design constraints imposedon the overall system. Skilled artisans may implement the describedfunctionality in varying ways for each particular application, but suchimplementation decisions should not be interpreted as causing adeparture from the scope of the present disclosure.

One of skill will further appreciate that the methods and apparatusdescribed herein may be applied to any fluidic system making use ofbiopolymer molecules in situations where clogs may develop.

The various illustrative logical blocks, modules, and circuits describedin connection with the embodiments disclosed herein may be implementedor performed with a general purpose processor, a digital signalprocessor (DSP), an application specific integrated circuit (ASIC), afield programmable gate array (FPGA) or other programmable logic device,discrete gate or transistor logic, discrete hardware components, or anycombination thereof designed to perform the functions described herein.A general purpose processor may be a microprocessor, but in thealternative, the processor may be any conventional processor,controller, microcontroller, or state machine. A processor may also beimplemented as a combination of computing devices, e.g., a combinationof a DSP and a microprocessor, a plurality of microprocessors, one ormore microprocessors in conjunction with a DSP core, or any other suchconfiguration.

In one or more example embodiments, the functions and methods describedmay be implemented in hardware, software, or firmware executed on aprocessor, or any combination thereof. If implemented in software, thefunctions may be stored on or transmitted over as one or moreinstructions or code on a computer-readable medium. Computer-readablemedia include both computer storage media and communication mediaincluding any medium that facilitates transfer of a computer programfrom one place to another. A storage medium may be any available mediathat can be accessed by a computer. By way of example, and notlimitation, such computer-readable media can comprise RAM, ROM, EEPROM,CD-ROM or other optical disk storage, magnetic disk storage or othermagnetic storage devices, or any other medium that can be used to carryor store desired program code in the form of instructions or datastructures and that can be accessed by a computer. Also, any connectionis properly termed a computer-readable medium. For example, if thesoftware is transmitted from a website, server, or other remote sourceusing a coaxial cable, fiber optic cable, twisted pair, digitalsubscriber line (DSL), or wireless technologies such as infrared, radio,and microwave, then the coaxial cable, fiber optic cable, twisted pair,DSL, or wireless technologies such as infrared, radio, and microwave areincluded in the definition of medium. Disk and disc, as used herein,includes compact disc (CD), laser disc, optical disc, digital versatiledisc (DVD), floppy disk and Blu-ray disc where disks usually reproducedata magnetically, while discs reproduce data optically with lasers.Combinations of the above should also be included within the scope ofcomputer-readable media.

The foregoing description details certain embodiments of the systems,devices, and methods disclosed herein. It will be appreciated, however,that no matter how detailed the foregoing appears in text, the systems,devices, and methods can be practiced in many ways. As is also statedabove, it should be noted that the use of particular terminology whendescribing certain features or aspects of the invention should not betaken to imply that the terminology is being re-defined herein to berestricted to including any specific characteristics of the features oraspects of the technology with which that terminology is associated.

It will be appreciated by those skilled in the art that variousmodifications and changes may be made without departing from the scopeof the described technology. Such modifications and changes are intendedto fall within the scope of the embodiments. It will also be appreciatedby those of skill in the art that parts included in one embodiment areinterchangeable with other embodiments; one or more parts from adepicted embodiment can be included with other depicted embodiments inany combination. For example, any of the various components describedherein and/or depicted in the Figures may be combined, interchanged orexcluded from other embodiments.

With respect to the use of substantially any plural and/or singularterms herein, those having skill in the art can translate from theplural to the singular and/or from the singular to the plural as isappropriate to the context and/or application. The varioussingular/plural permutations may be expressly set forth herein for sakeof clarity.

It will be understood by those within the art that, in general, termsused herein are generally intended as “open” terms (e.g., the term“including” should be interpreted as “including but not limited to,” theterm “having” should be interpreted as “having at least,” the term“includes” should be interpreted as “includes but is not limited to,”etc.). It will be further understood by those within the art that if aspecific number of an introduced claim recitation is intended, such anintent will be explicitly recited in the claim, and in the absence ofsuch recitation no such intent is present. For example, as an aid tounderstanding, the following appended claims may contain usage of theintroductory phrases “at least one” and “one or more” to introduce claimrecitations. However, the use of such phrases should not be construed toimply that the introduction of a claim recitation by the indefinitearticles “a” or “an” limits any particular claim containing suchintroduced claim recitation to embodiments containing only one suchrecitation, even when the same claim includes the introductory phrases“one or more” or “at least one” and indefinite articles such as “a” or“an” (e.g., “a” and/or “an” should typically be interpreted to mean “atleast one” or “one or more”); the same holds true for the use ofdefinite articles used to introduce claim recitations. In addition, evenif a specific number of an introduced claim recitation is explicitlyrecited, those skilled in the art will recognize that such recitationshould typically be interpreted to mean at least the recited number(e.g., the bare recitation of “two recitations,” without othermodifiers, typically means at least two recitations, or two or morerecitations). Furthermore, in those instances where a conventionanalogous to “at least one of A, B, and C, etc.” is used, in generalsuch a construction is intended in the sense one having skill in the artwould understand the convention (e.g., “a system having at least one ofA, B, and C” would include but not be limited to systems that have Aalone, B alone, C alone, A and B together, A and C together, B and Ctogether, and/or A, B, and C together, etc.). In those instances where aconvention analogous to “at least one of A, B, or C, etc.” is used, ingeneral such a construction is intended in the sense one having skill inthe art would understand the convention (e.g., “a system having at leastone of A, B, or C” would include but not be limited to systems that haveA alone, B alone, C alone, A and B together, A and C together, B and Ctogether, and/or A, B, and C together, etc.). It will be furtherunderstood by those within the art that virtually any disjunctive wordand/or phrase presenting two or more alternative terms, whether in thedescription, claims, or drawings, should be understood to contemplatethe possibilities of including one of the terms, either of the terms, orboth terms. For example, the phrase “A or B” will be understood toinclude the possibilities of “A” or “B” or “A and B.”

While various aspects and embodiments have been disclosed herein, otheraspects and embodiments will be apparent to those skilled in the art.The various aspects and embodiments disclosed herein are for purposes ofillustration and are not intended to be limiting.

1. A method for enhancing fluid flow, the method comprising: movingbiopolymer molecules into contact with at least one fluidic channel inor on a device, whereby clogging occurs in the device due to coiling oraggregation of the biopolymer molecules or adsorption to or tangling ofthe biopolymer molecules around the channels or any other nano- ormicro-features inside the channel or fluidic device; and directing alight source at a region of the device in which said clogging hasoccurred in a manner effective to photocleave biopolymer molecules thatcontribute to said clogging, thereby facilitating removal or reductionof said clogging.
 2. The method of claim 1, further comprising applyinga motive force to fluid in the region of the device in a mannereffective to flush the photocleaved biopolymer molecules from the regionof the device comprising said clogging.
 3. The method of claim 2,wherein the motive force comprises an electrostatic force, a pneumaticforce, a capillary force, or any combination thereof.
 4. The method ofclaim 1, wherein the biopolymer molecules comprise DNA or RNA.
 5. Themethod of claim 1, further comprising labeling the biopolymer moleculeswith an indicator to facilitate photocleavage of the biopolymermolecules when exposed to the light source, wherein the light source isconfigured to generate a light matched with the indicator to enhancephotocleaving capabilities.
 6. The method of claim 5, wherein theindicator used to label the biopolymer molecules comprises one or moreof YOYO-1, YOYO-3, TOTO, methylene blue, Cu, Rh, compounds useful forphotodynamic therapy, and other photon absorbers capable of facilitatingcleavage of the biopolymer upon irradiation with photons.
 7. The methodof claim 6, wherein the indicator is YOYO-1 and the light source has awavelength of one of about 473 nm or about 488 nm.
 8. The method ofclaim 1, further comprising detecting a clogged or reduced flowcondition.
 9. The method of claim 8, wherein the detection comprisesidentifying that a transport of the biopolymer molecules through thedevice falls below a threshold transport value.
 10. The method of claim8, wherein the detection comprises direct imaging of at least onefluidic channel in or on the device to indicate clogging.
 11. The methodof claim 1, wherein a cleaning of the region of the device in which theclogging has occurred is implemented in an automatic fashion at one of apredetermined time or a predetermined transport threshold.
 12. Themethod of claim 1, further comprising positioning the light source in amanner effective to minimize exposure of the device other than theregion of the device in which said clogging has occurred to the lightsource.
 13. An apparatus for enhancing fluid flow, the apparatuscomprising: a light source configured to generate a light beamconfigured to photocleave biopolymer molecules; and a controllerconfigured to: control a movement of the biopolymer molecules intocontact with at least one fluidic channel in or on a device, wherebyclogging occurs in the device due to coiling or aggregation of thebiopolymer molecules or adsorption to or tangling of the biopolymermolecules around the channels or other nano- or micro-patterned featuresinside the channel or fluidic device; direct the light source at aregion of the device in which a clog of biopolymer molecules has formed;and activate the light source to generate the light beam for an amountof time to facilitate a photocleaving of the biopolymer moleculesforming said clog.
 14. The apparatus of claim 13, further comprising amotive force generator configured to generate a motive force, whereinthe controller is configured to control a movement of the biopolymermolecules via the generated motive force and wherein the controller isfurther configured to apply the motive force to fluid in the region ofthe device in which said clog occurred in a manner effective to flushthe photocleaved biopolymer molecules from the region.
 15. The apparatusof claim 14, wherein the motive force comprises an electrostatic force,a pneumatic force, a capillary force, or any combination thereof. 16.The apparatus of claim 14, wherein the motive force generator isconfigured to generate one of an electrostatic force or a pneumaticforce.
 17. The apparatus of claim 13, wherein the light beam generatedby the light source has a wavelength of one of about 473 nm or about 488nm.
 18. The apparatus of claim 13, wherein the biopolymer moleculescomprise DNA or RNA.
 19. The apparatus of claim 13, further comprising adetector configured to detect a clog or reduced flow condition throughthe at least one fluidic channel in or on the device.
 20. The apparatusof claim 19, wherein the detector is further configured to identify thata transport of biopolymer molecules through the at least one fluidicchannel in or on the device falls below a threshold transport value. 21.The apparatus of claim 20, wherein the detector is further configured todirectly image the at least one fluidic channel in or on the device toindicate the clog.
 22. The apparatus of claim 13, wherein the controlleris configured to operate the light source and enhance fluid flow in atautomatic fashion at one of a predetermined time or a predeterminedtransport threshold.
 23. The apparatus of claim 13, further comprisingan x-y-z translation motor configured to position the light source in amanner effective to minimize exposure of the device other than theregion of the device in which a clog of biopolymer molecules has formedto the light source and further configured to allow positioning of thelight source at any location in relation to the device.
 24. An apparatusfor characterizing a biopolymer molecule, the apparatus comprising: afluidic device comprising a detection region comprising at least onechannel, and further comprising the biopolymer molecule; a motive forcegenerator to move biopolymer molecules into the detection region;wherein a clog of biopolymer molecules occurs in the fluidic devicehampering further flow of new biopolymer molecules to the detectionregion; a detection system for determining a characteristic of thebiopolymer molecules in the detection region; a light source set todeliver a light comprising a configuration for photocleaving thebiopolymer molecules forming the clog; a light delivery system todeliver the light to any region of the fluidic device; a positioningsystem to target the detection system to the detection region forcharacterization of the biopolymer molecules, and to target the lightcomprising the photocleaving configuration to a region of the devicewhere the clog has formed; and a controller configured to: activate themotive force generator to move the biopolymer molecules into thedetection region; direct the detection system to the detection region;activate the detection system to determine the characteristics of thebiopolymer molecules; direct the light source configured forphotocleaving biopolymer molecules to the region where the clog hasformed; activate the light source to generate a light for photocleavingbiopolymer molecules forming the clog; and activate the motive forcegenerator after activating the light source to flush out thephotocleaved biopolymer molecules wherein additional new biopolymermolecules flow into the detection region for characterization after themotive force generator flushes out the photocleaved biopolymermolecules. 25.-27. (canceled)